def _atmos_ (atmFiles, outFile=None, commentChar='#', extract='*', where=None, zToA=None, pRatio=None, zGrid=None, format=None, saveVMR=False, pT=False, verbose=False):
if isinstance(where, str):
# replace acronyms with names used in namelist file
where = atmos_short2long_name(where)
profileList = get_profile_list (atmFiles, commentChar, extract, where, verbose)
if zToA or pRatio or zGrid:
profileList = reGridProfiles (profileList, zToA, zGrid, pRatio)
if verbose:
for prof in profileList: print prof
atmos1d = Atmos1D(profileList)
out = open_outFile (outFile, commentChar)
if format in ('namelist', 'nml'):
write_atmos_namelist (out, atmos1d, saveVMR)
elif format=='xy':
write_atmos_xy (out, atmos1d, pT, saveVMR)
else:
from pprint import pprint
pprint(atmos1d.__dict__, out)
# close the output file (if its not stdout)
if outFile: out.close()
def save_optDepth_xy (vGrid, optDepth, outFile=None, atmos=None, nanometer=False, yOnly=False, flipUpDown=False, commentChar='#'):
""" Save optical depth (vs wavenumber or wavelength) in ascii tabular format. """
out = open_outFile (outFile, commentChar)
nLevels = len(atmos.z)
nGas = len(atmos.gases)
if flipUpDown:
if len(optDepth.shape)==2: optDepth = np.fliplr(optDepth) # swap columns
comments = ['altitudes [km]: ' + nLevels*' %10.1f' % tuple(unitConversion(atmos.z[::-1],'length',new='km')),
'temperatures [K]:' + nLevels*' %10.2f' % tuple(atmos.T[::-1]),
'pressures [mb]: ' + nLevels*' %10.4g' % tuple(unitConversion(atmos.p[::-1],'p',new='mb'))]
else:
comments = ['altitudes [km]: ' + nLevels*' %10.1f' % tuple(unitConversion(atmos.z,'length',new='km')),
'temperatures [K]:' + nLevels*' %10.2f' % tuple(atmos.T),
'pressures [mb]: ' + nLevels*' %10.4g' % tuple(unitConversion(atmos.p,'p',new='mb'))]
comments += ['gases: ' + nGas*' %10s' % tuple(atmos.gases),
'vcd [molec/cm^2]:' + nGas*' %10.2g' % tuple(atmos.vcd())]
if nanometer:
if yOnly:
writeArray (np.flipud(optDepth), out, comments=comments, format= '%10g')
else:
comments += ['%10s %10s' % ('wavelength','optical depth'), '%10s' % 'nm']
writeArray (np.flipud(paste(1e7/vGrid,optDepth)), out, comments=comments, format= '%10f %10g')
else:
if yOnly:
writeArray (optDepth, out, comments=comments, format= '%10g')
else:
comments += ['%10s %10s' % ('wavenumber','optical depth'), '%10s' % '1/cm']
writeArray (paste(vGrid,optDepth), out, comments=comments, format= '%10f %10g')
out.close()
def write_crossSections_xyy (crossSections, outFile=None, linePositions=None, interpolate='3', commentChar='#'):
""" Write cross section(s) to output (file) in tabular xy format.
(All cross sections of a given molecule (i.e., data for all p,T levels)
are interpolated to a common wavenumber grid and written to a single file) """
out = open_outFile (outFile, commentChar)
if outFile:
# print a summary
molecules = tuple([xs.get('molecule') for xs in crossSections])
sameMolec = np.alltrue([molecules[0] == other for other in molecules[1:]])
if sameMolec: out.write ( '%1s %-16s %s\n' % (commentChar, 'molecule:', molecules[0]))
lineShapes = tuple([xs.get('lineShape') for xs in crossSections])
sameShapes = np.alltrue([lineShapes[0] == other for other in lineShapes[1:]])
if sameShapes: out.write ( '%1s %-16s %s\n' % (commentChar, 'lineshape:', lineShapes[0]))
if isinstance(linePositions,np.ndarray):
out.write ( '%1s %i %s %f ... %f\n' % (commentChar, len(linePositions), 'lines in ', min(linePositions),max(linePositions)) )
# extract pressure and temperatures
nXS = len(crossSections)
pressures = tuple([unitConversion(xs.get('p',0.0),'p',new='mb') for xs in crossSections])
temperatures = tuple([xs.get('T',0.0) for xs in crossSections])
out.write ( commentChar+' pressure [mb]: ' + nXS*' %10g' % pressures + '\n')
out.write ( commentChar+' temperature [K]:' + nXS*' %10.2f' % temperatures + '\n')
out.write ( commentChar + '\n' )
# select an interpolation method
if interpolate.lower() in 'sb':
try: from scipy.interpolate import splrep, splev
except ImportError, msg: raise SystemExit, msg
else: intMethod = 'Spline interpolation (scipy splrep/splev)'
def write_voigtLines (positions, strengths, gammaL, gammaD, pressure, temperature, molecule, outFile=None, commentChar='#'):
""" Write Voigt line parameters (strengths, Lorentz and Gaussian widths vs line positionsp. """
out = open_outFile (outFile, commentChar)
out.write ('%s %s %s\n' % (commentChar, "molecule:", molecule))
out.write ('%s %s %-12g\n' % (commentChar, "pressure [mb]: " , unitConversion(pressure,'p', new='mb')))
out.write ('%s %s %8.2f\n' % (commentChar, "temperature [K]: ", temperature))
out.write ('%s %10s %11s %11s %11s\n' % (commentChar, "position", "strength", "gammaL", "gammaG"))
format = '%12f %11.3e %11.3g %11.3g\n'
for v,S, gL, gG in zip(positions, strengths, gammaL, gammaD): out.write ( format % (v,S,gL,gG) )
# close the output file (if its not stdout)
if outFile: out.close()
def write_strengths (positions, strengths, strRef, temperature, tempRef, molecule, outFile=None, commentChar='#'):
""" Write line strengths (for two temperatures) vs line positions. """
out = open_outFile (outFile, commentChar)
out.write ('%s %s %s\n' % (commentChar, "molecule:", molecule))
out.write ('%s %s %8.2f %s\n' % (commentChar, "temperature T_ref:" , tempRef, "K"))
out.write ('%s %s %8.2f %s\n' % (commentChar, "temperature T: ", temperature, "K"))
out.write ('%s %10s %23s\n' % (commentChar, "position", " S(T_ref) |S(T)- S(T_ref)|"))
format = '%12f %11.3e %10.2e 0\n'
for v,S0,S in zip(positions, strRef, strengths):
#out.write ( format % (v,S0,S) )
if S>S0: out.write ( format % (v,S0,S-S0) )
else: out.write ( format % (v,S0,S0-S) )
# close the output file (if its not stdout)
if outFile: out.close()
def write_crossSections_xy (crossSections, outFile=None, linePositions=None, commentChar='#'):
""" Write cross section(s) to output (file) in tabular xy format.
(Cross sections of a given molecule (i.e., data for all p,T levels) are written to a individual files) """
# extract attributes like pressure and temperatures
nXS = len(crossSections)
molecules = tuple([xs.get('molecule') for xs in crossSections])
pressures = tuple([unitConversion(xs.get('p',0.0),'p',new='mb') for xs in crossSections])
temperatures = tuple([xs.get('T',0.0) for xs in crossSections])
lineShapes = tuple([xs.get('lineShape') for xs in crossSections])
if isinstance(linePositions,np.ndarray):
lineInfo = '%i %s %f ... %f' % (len(linePositions), 'lines in ', min(linePositions),max(linePositions))
else:
lineInfo = ''
for l, xs in enumerate(crossSections):
if isinstance(outFile,str) and '.' in outFile:
outRoot, outExt = os.path.splitext(outFile)
oFile = '%s_%2.2i_%gmb_%.1fK%s' % (outRoot, l+1, pressures[l], temperatures[l], outExt)
else:
oFile = '%s_%gmb_%.1fK.%s' % (molecules[l], pressures[l], temperatures[l], 'xs')
out = open_outFile (oFile, commentChar)
# print a summary
out.write ( '%1s %-16s %s\n' % (commentChar, 'molecule:', molecules[l]))
out.write ( '%1s %-16s %s\n' % (commentChar, 'lineshape:', lineShapes[l]))
if lineInfo: out.write ( '%1s %s\n' % (commentChar, lineInfo))
out.write ( commentChar+' pressure [mb]: ' + ' %10g' % pressures[l] + '\n')
out.write ( commentChar+' temperature [K]:' + ' %10.2f' % temperatures[l] + '\n')
out.write ( commentChar + '\n' )
# extract cross section spectra and save in list
yyy = xs['y']
nxy = len(yyy)-1
xLow, xHigh = crossSections[0]['x'].limits()
xLo, xHi = float(xLow/nxy), float(xHigh/nxy)
# and write cross section vs wavenumber
out.write ( '%1s%12s %15s\n' % (commentChar, 'wavenumber', 'cross section') )
format = ' %12f %12.6g\n'
for i,y in enumerate(yyy):
x = i*xHi + (nxy-i)*xLo
out.write (format % (x,y))
if outFile: out.close()
def print_lines(outFile, Lines, dataFile, molecule, format="", commentChar="#"):
if "hit" in lower(dataFile):
xUnit, TRef, pRef = "cm-1", 296.0, 1013.25
elif "sao" in lower(dataFile):
xUnit, TRef, pRef = "cm-1", 296.0, 1013.25
elif "geisa" in lower(dataFile):
xUnit, TRef, pRef = "cm-1", 296.0, 1013.25
elif "jpl" in lower(dataFile):
xUnit, TRef, pRef = "MHz", 300.0, 1013.0
else:
raise SystemExit, "unknown database type!"
# check if output file extension indicates the format
if outFile:
outFileExt = os.path.splitext(outFile)[1]
if not format and lower(outFileExt).startswith(".vs"):
format = outFileExt[1:]
print "format automatically determined from output file extension ", format
if lower(format).startswith("vs"):
if molecule:
write_lines_xy(outFile, Lines, dataFile, format, TRef, pRef, molecule, commentChar)
else:
if outFile:
print "\nWARNING: specified output filename will be ignored!\n (lines will be saved to files with names defined by molecule and format)\n"
lineLists = split_molecules(Lines, dataFile) # actually this returns a dictionary!
for molec, lines in lineLists.items():
outFile = molec + os.path.extsep + format
write_lines_xy(outFile, lines, dataFile, format, TRef, pRef, molec, commentChar)
else:
# save line extract in original format
commentChar = "00"
if "hit" in dataFile:
if lower(format).startswith("g"):
raise SystemExit, "\nERROR --- extract: no format conversion hitran -> geisa"
elif "geisa" in dataFile:
commentChar = 5 * commentChar
if lower(format).startswith("h"):
raise SystemExit, "\nERROR --- extract: no format conversion geisa -> hitran"
else:
if lower(format).startswith("g") or lower(format).startswith("h"):
raise SystemExit, "\nERROR --- extract: no format conversion ??? -> hitran"
out = open_outFile(outFile, commentChar)
if "hit" in dataFile.lower():
if len(Lines[0].rstrip()) == 100: # old hitran versions <=2000
out.write(
"%3s%12s%10s%10s%5s%5s%10s%4s%8s%3s%3s%9s%9s%3s%6s\n"
% (
"000",
"wavenumber",
"S",
"A",
"air",
"self",
"Energy",
"n",
"pShift",
"uV",
"lV",
"uL",
"lL",
"er",
"ref",
)
)
else: # new hitran versions >=2004
out.write(
"%3s%12s%10s%10s%5s%5s%10s%4s%8s%15s%15s%15s%15s%6s%12s %s7%7s\n"
% (
"000",
"wavenumber",
"S",
"A",
"air",
"self",
"Energy",
"n",
"pShift",
"upVib",
"loVib",
"upLocal",
"loLocal",
"err",
"ref",
"usw",
"lsw",
)
)
for line in Lines:
out.write(line)
if outFile:
out.close()
return
def write_lines_xy(outFile, lines, dataFile, job="vS", TRef=0, pRef=0, molecule="", commentChar="#"):
""" Print 'core' line parameters, i.e., positions vs strengths, and optionally energies, airWidths, tempExponents. """
# open an output file if explicitely specified (otherwise use standard output)
out = open_outFile(outFile, commentChar)
if molecule:
out.write("%s %s %s\n" % (commentChar, "molecule:", molecule))
# reference pressure and temperature of database
if TRef:
out.write("%s %s %8.2f %s\n" % (commentChar, "temperature:", TRef, "K"))
if pRef:
out.write("%s %s %8.2f %s\n" % (commentChar, "pressure: ", pRef, "mb"))
# extract most important numeric line parameters
positions, strengths, energies, airWidths, selfWidths, tempDep, isoNr = core_parameters(lines, dataFile)
# some statistical information
nLines = len(positions)
out.write("%s %-30s %12i\n" % (commentChar, "number of lines: ", nLines))
out.write("%s %-30s %12.3g%13.3g\n" % (commentChar, "min, max line strength: ", min(strengths), max(strengths)))
out.write("%s %s %s\n" % (commentChar, "format:", job))
if "a" in job:
out.write(
"%s %-30s %12.3f%13.3f\n" % (commentChar, "min, max airbroad. widths: ", min(airWidths), max(airWidths))
)
out.write(
"%s %-30s %12.3f%13.3f\n" % (commentChar, "min, max selfbroad. widths: ", min(selfWidths), max(selfWidths))
)
out.write("%s %-30s %12.3f%13.3f\n" % (commentChar, "min, max temp. exponent: ", min(tempDep), max(tempDep)))
if outFile:
print "%-8s %8i %s %11.3g %s %-11.3g %s %s" % (
molecule,
nLines,
" lines with",
min(strengths),
"< S <",
max(strengths),
" writing to file",
outFile,
)
#
if job == "vSEani":
format = "%12f %11.3e %11.5f %8.5f %7.4f %3i\n"
out.write(
"%1s %10s %11s %11s %8s %7s %3s\n"
% (commentChar, "position", "strength", "energy", "airWidth", "Tdep", "iso")
)
out.write("%1s %10s %11s %11s %8s %7s\n" % (commentChar, "cm-1", "cm-1/cm-2", "cm-1", "cm-1", ""))
for l in xrange(nLines):
out.write(format % (positions[l], strengths[l], energies[l], airWidths[l], tempDep[l], isoNumber[l]))
elif job == "vSEan":
format = "%12f %11.3e %11.5f %8.5f %7.4f\n"
out.write("%1s %10s %11s %11s %8s %7s\n" % (commentChar, "position", "strength", "energy", "airWidth", "Tdep"))
out.write("%1s %10s %11s %11s %8s %7s\n" % (commentChar, "cm-1", "cm-1/cm-2", "cm-1", "cm-1", ""))
for l in xrange(nLines):
out.write(format % (positions[l], strengths[l], energies[l], airWidths[l], tempDep[l]))
elif job == "vSEasni":
format = "%12f %11.3e %11.5f %8.5f %8.5f %7.4f %4i\n"
out.write(
"%1s %10s %11s %11s %8s %8s %7s %4s\n"
% (commentChar, "position", "strength", "energy", "airWidth", "selfWidth", "Tdep", "iso")
)
out.write("%1s %10s %11s %11s %8s %8s %7s\n" % (commentChar, "cm-1", "cm-1/cm-2", "cm-1", "cm-1", "cm-1", ""))
for l in xrange(nLines):
out.write(
format % (positions[l], strengths[l], energies[l], airWidths[l], selfWidths[l], tempDep[l], isoNr[l])
)
elif job == "vSEasn":
format = "%12f %11.3e %11.5f %8.5f %8.5f %7.4f\n"
out.write(
"%1s %10s %11s %11s %8s %8s %7s\n"
% (commentChar, "position", "strength", "energy", "airWidth", "selfWidth", "Tdep")
)
out.write("%1s %10s %11s %11s %8s %8s %7s\n" % (commentChar, "cm-1", "cm-1/cm-2", "cm-1", "cm-1", "cm-1", ""))
for l in xrange(nLines):
out.write(format % (positions[l], strengths[l], energies[l], airWidths[l], selfWidths[l], tempDep[l]))
elif job == "vSEa":
format = "%12f %11.3e %11.5f %8.5f\n"
for l in xrange(nLines):
out.write(format % (positions[l], strengths[l], energies[l], airWidths[l]))
elif job == "vSE":
format = "%12f %11.3e %11.5f\n"
for l in xrange(nLines):
out.write(format % (positions[l], strengths[l], energies[l]))
else:
format = "%12f %11.3e\n"
for l in xrange(nLines):
out.write(format % (positions[l], strengths[l]))
# close the output file (if its not stdout)
if outFile:
out.close()
return
from command_parser import parse_command, standardOptions
opts = standardOptions + [ # h=help, c=commentChar, o=outFile
{'ID': 'i', 'name': 'isoNr', 'type': IntType, 'default': 0},
{'ID': 'm', 'name': 'molNr', 'type': IntType, 'default': 0},
{'ID': 'S', 'name': 'strMin', 'type': FloatType, 'default': 0.0, 'constraint': 'strMin>=0.0'},
{'ID': 'x', 'name': 'xLimits', 'type': Interval, 'default': Interval(0.0,99999.9), 'constraint': 'xLimits.lower>=0.0'}
]
files, options, commentChar, outFile = parse_command (opts, 1)
for opt in opts:
if opt.has_key('name') and opt.has_key('type'): exec opt['name'] + ' = ' + repr(options.get(opt['name']))
if options.has_key('h'):
print __doc__%globals(); raise SystemExit, " end of hitran help"
elif molNr or xLimits.size()<50000.0:
# Read lines from HITRAN line parameter file
lines = extract_hitran (files[0], xLimits, molNr, isoNr, strMin)
print len(lines), ' lines'
else:
# at least molecule or wavenumber range needed
raise SystemExit, ' ERROR: neither molecule nor wavenumber range specified!'
# open an output file if explicitely specified (otherwise use standard output)
out = open_outFile (outFile, commentChar='00')
# print extracted lines
for line in lines: out.write (line)
# close the output file (if its not stdout)
if outFile: out.close()
